Coverage evaluation of universal bacterial primers using the metagenomic datasets.

BMC Microbiology
Dan-Ping MaoZhe-Xue Quan

Abstract

The coverage of universal primers for the bacterial 16S rRNA gene plays a crucial role in the correct understanding of microbial community structure. However, existing studies on primer coverage are limited by the lack of appropriate databases and are restricted to the domain level. Additionally, most studies do not account for the positional effect of single primer-template mismatches. In this study, we used 7 metagenomic datasets as well as the Ribosomal Database Project (RDP) to assess the coverage of 8 widely used bacterial primers. The coverage rates for bacterial primers were found to be overestimated by previous studies that only investigated the RDP because of PCR amplification bias in the sequence composition of the dataset. In the RDP, the non-coverage rates for all primers except 27F were ≪6%, while in the metagenomic datasets, most were ≫10%. If one considers that a single mismatch near the 3' end of the primer might greatly reduce PCR efficiency, then some phylum non-coverage rates would change by more than 20%. Primer binding-site sequence variants that could not pair with their corresponding primers are discussed. Our study revealed the potential bias introduced by the use of universal bacterial primers in the as...Continue Reading

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Citations

Mar 22, 2013·World Journal of Microbiology & Biotechnology·Dan-Ning ZengZhe-Xue Quan
May 17, 2013·Briefings in Bioinformatics·Jing WangPeter J Lockhart
Jul 19, 2013·Genome Research·Catherine A LozuponeRob Knight
Aug 12, 2014·PloS One·Anastasia S KhodakovaAdrian Linacre
Jan 29, 2014·Microbial Informatics and Experimentation·Hilde VinjeLars Snipen
Jul 3, 2013·World Journal of Microbiology & Biotechnology·Gurikar ChennappaM Y Sreenivasa
Nov 28, 2013·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hiroshi MoriKen Kurokawa
Feb 18, 2014·Applied Microbiology and Biotechnology·Xiao-Ran LiZhe-Xue Quan
Oct 2, 2015·Mediators of Inflammation·Tamsyn DerrickMartin J Holland
Aug 28, 2015·Environmental Entomology·Omer LavyElad Chiel
Aug 24, 2016·Frontiers in Nutrition·Jacobo de la Cuesta-Zuluaga, Juan S Escobar
Sep 7, 2016·Clinical Nutrition : Official Journal of the European Society of Parenteral and Enteral Nutrition·Li LiShawn Somerset
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May 20, 2018·World Journal of Microbiology & Biotechnology·Ngoc Tuan TranShan-Gong Wu
Dec 21, 2017·International Journal of Microbiology·Anna DolomanCharles D Miller
Oct 18, 2015·Applied and Environmental Microbiology·Jiarong GuoJames M Tiedje
Apr 25, 2018·Mediators of Inflammation·Anna PiccaEmanuele Marzetti
Nov 12, 2019·Frontiers in Plant Science·Rares LucaciuThomas Rattei
Jan 23, 2020·PloS One·Michelle A NottScott W Tighe
Dec 18, 2019·Clinical Chemistry·Robert Schlaberg
Mar 8, 2017·PeerJ·Marcel Martinez-PorchasFrancisco Vargas-Albores

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Datasets Mentioned

BETA
J01695

Methods Mentioned

BETA
PCR
amplicon sequencing

Software Mentioned

BLAST
Phyla
BROWSERS
Perl
Probe Match ( ARB )
CAMERA
Probe Match
script
Basic Local Alignment Search Tool ( BLAST )
scripts

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